app-splitshells

dwi images contsists of several diffusion weight images (volumes) with different gradient directions (bvecs) and strenghth (bvals). Some processing can only run on specific bvals (aka "single shell"). This service will look for volumes with specific bvals and pull those images to create a "single shell" image. bvecs are often similar but not exactly the same. This App also allows you to specify range of bvals to be rounded to the nearest 100s (like 1980 to 2000, for example).

Authors

• Lindsey Kitchell ([email protected])
• Soichi Hayashi ([email protected])

Project directors

• Franco Pestilli ([email protected])

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.17 via the "Execute" tab.

Running Locally (on your machine)

1. git clone this repo.
2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
        "shell": 2500,
        "b0_max": 200,
        "bvals_round": 100,
        "bvals": "input/dwi/dwi.bvals",
        "bvecs": "input/dwi/dwi.bvecs",
        "dwi": "input/dwi/dwi.nii.gz"
}

3. Launch the App by executing main

./main

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5a050a00eec2b300611abff3 && mv 5a050a00eec2b300611abff3 input/dwi

Output

This App will generate dwi.nii.gz, dwi.bvecs, anb dwi.bvals on the current working directory.

Dependencies

This App only requires singularity to run. If you don't have singularity, you will need to install following dependencies.

• Matlab: https://www.mathworks.com/products/matlab.html
• VISTASOFT: https://github.com/vistalab/vistasoft/
• jsonlab: https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files?w.mathworks.com